#include <iostream>
#include <string>
#include <fstream>
#include <iostream>
#include <limits>
#include <string>
#include <cstdio>
#include <boost/program_options.hpp>
#include <boost/filesystem/path.hpp>
#include "get_arg.h"


// link with -lboost_filesystem-gcc -lboost_program_options-gcc
// program_options_helper.cpp



// my functions
#define DEBUG_LEVEL 6
#include <debug_func.h>
#include <print_error.h>
#include <program_options_helper.h>

using std::ofstream;
using std::ifstream;
using std::cout;
using std::string;
using std::vector;
using std::cerr;
using namespace program_options_helper;
namespace po = boost::program_options_lg;


//_______________________________________________________________________________________

//		process_command_line_options

//				from command line
//				Created [9/13/2001]

//_______________________________________________________________________________________



bool process_command_line_options(int argc, char* argv[], t_program_args& args)
{
	//
	//	Mandatory arguments
	//
	//po::options_description mandatory_args("Mandatory Arguments");
	//mandatory_args.add_options()


	//
	//	Optional arguments
	//
	args.optional_args.add_options()
	("input_file,i",			po::value<string>(&args.file_input)
										->set_name("FILE")
										->default_value("STDIN"),
									"File containing alignment results.")
	("results_summary,R",		po::value<string>(&args.results_summary)
										->set_name("FILE"),
									"Write out summary of relationship pairs greater than "
							   		"the set thresholds.")
	("len_threshold,l",			po::value<unsigned>(&args.len_threshold)
										->set_name("NUMBER")
										->default_value(50),
									"Ignore results with number of aligned residues < "
									"NUMBER.\1"
									"NUMBER = 0 means do not filter.")
	("coverage_residues,r",		po::value<float>(&args.residues_coverage)
										->set_name("FRACTION")
										->default_value(0.60),
									"Print results where aligned residues covers more than "
									"this fraction of residues in the LONGER sequence.\1"
									"(I.e. Fragments are discarded.)")
	("coverage_fragment,f",		po::value<float>(&args.fragment_coverage)
										->set_name("FRACTION")
										->default_value(0.75),
									"Print results where aligned residues covers more than "
									"this fraction of residues in the SHORTER sequence.\1"
									"(I.e. Fragments are kept.)")
	("coverage_both,b",			po::bool_switch(&args.coverage_both),
									"Both coverage requirements have"
									"need to be satisfied at the same time for any "
									"sequence.)")
	("#comment,#",				po::value<string>(&args.comment_letters)
										->set_name("LETTERS")
										->default_value("#"),
									"Use one of these letters to begin a "
									"commented line.");

	args.add_std_options();

	//	Parse all arguments
	//
	po::options_description all_args("");
	all_args

				//	Mandatory arguments
				//.add(mandatory_args)

				//	Optional arguments
				.add(args.optional_args);

				//	Positional arguments
				//.add(positional_args);

	po::variables_map vm;
	po::store(po::command_line_parser(argc, argv)
								.options(all_args)

								//	Positional arguments
								//.positional(positional_parser)

								.run(), vm);
	po::notify(vm);


	if (vm.count("version"))
	{
		print_version(cerr, *argv, "1.3\n"
			"\tHistory: \n\n"
			"\tv 1.0\1"
			"03-07-2005\1"
			"Filter align results which are beyond reasonable thresholds.\n"
			"\tv 1.1\1"
			"23-08-2005\1"
			"Accepts a single file rather than a path.\n"
			"\tv 1.2\1"
			"04-01-2006\1"
			"For Andreas: Hash start comment lines. Fix bugs in handling input. "
			"Upgrade to common code for sequence pair identifiers\n"
			"\tv 1.3\1"
			"27-03-2006\1"
			"Comments can begin with user-defined letters. Defaults to hash '#'\n"
			);
		return false;
	}

	if (vm.count("help"))
	{
		string exe_description =
							"Takes an align result FILE produced by seq_pairs_align, "
							"screens for those which are greater than the specified "
							"thresholds.\n"
							"The output is sent to STDOUT\n"
							"Set any threshold to zero "
							" to avoid filtering on that parameters"
							"Defaults to --coverage_residues 0.6 --coverage_fragment 0.75 "
							"meaning that sequences can align EITHER over 60% or more of the "
							"longer sequence or 75% or more of the shorter sequence.\n"
							"If '--coverage_both' is specified, the alignment of each "
							"sequence pair has to meet BOTH coverage thresholds.\n";

		//
		//	Only output visible arguments for help string
		//
		po::options_description visible_args("");
		visible_args

					//	Mandatory arguments
					//.add(mandatory_args)

					//	Optional arguments
					.add(args.optional_args);


		print_usage(cerr, string(*argv),    "[OPTIONS] FILES ",
							visible_args, exe_description, 80);
		return false;
	}

	// test for > threshold so everything will pass
	//check_required_options(vm, mandatory_args);
	if (args.fragment_coverage == 0.0 ||
		args.residues_coverage == 0.0)
	{
		args.coverage_both = true;
	}


	args.open_err_log();

	return true;
}




